Merge pull request #20 from BCDA-APS/15-APS-U-update

update project for APS-U

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# Set update schedule for GitHub Actions
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/code.yml

@@ -0,0 +1,100 @@
+name: Unit Tests & Code Coverage
+
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch: # allow manual triggering
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  lint:
+    name: Code style
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: ruff
+        uses: chartboost/ruff-action@v1
+
+  matrix:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    needs: lint
+    strategy:
+      matrix:
+        python-version:
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          # - "3.12"  # TODO: dm package not ready
+      max-parallel: 5
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create Python ${{ matrix.python-version }} environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-environment: true
+          cache-environment-key: env-key-${{ matrix.python-version }}
+          condarc: |
+            channel-priority: flexible
+          environment-file: environment.yml
+          environment-name: anaconda-test-env-py-${{ matrix.python-version }}
+          create-args: >-
+            caproto
+            coveralls
+            pytest
+            pytest-cov
+            python=${{ matrix.python-version }}
+            setuptools-scm
+
+      - name: Run tests with pytest & coverage
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          coverage run --concurrency=thread --parallel-mode -m pytest -vvv --exitfirst .
+          coverage combine
+          coverage report --precision 3
+
+      - name: Upload coverage data to coveralls.io
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          micromamba list coveralls
+          which coveralls
+          coveralls debug
+          coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
+          COVERALLS_PARALLEL: true
+
+  # https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
+  coveralls:
+    name: Report unit test coverage to coveralls
+    needs: matrix
+    runs-on: ubuntu-latest
+    container: python:3-slim
+
+    steps:
+      - name: Gather coverage and report to Coveralls
+        run: |
+          set -vxeuo pipefail
+          echo "Finally!"
+          pip3 install --upgrade coveralls
+          # debug mode: output prepared json and reported files list to stdout
+          # https://coveralls-python.readthedocs.io/en/latest/troubleshooting.html
+          coveralls debug
+          coveralls --service=github --finish
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/docs.yml

@@ -0,0 +1,71 @@
+name: Publish Sphinx docs to GitHub Pages
+# see: https://github.com/marketplace/actions/sphinx-to-github-pages
+
+on:
+  # Build the docs on pushes to main branch, PRs to main branch, and new tags.
+  # Publish only on demand.
+  push:
+    branches:
+      - main
+    tags:
+      - '*'  # all tags
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:   # allow manual triggering
+    inputs:
+      deploy:
+        description: 'Deploy documentation'
+        type: boolean
+        required: true
+        default: false
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+
+  pages:
+    name: Publish documentation
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Deploy Information
+      if: ${{ github.event.inputs.deploy }}
+      run: |
+        echo "The docs will be published from this workflow run."
+
+    # - name: Install pandoc
+    #   run: |
+    #     sudo apt-get update && \
+    #     sudo apt-get -y install pandoc
+
+    - name: Set time zone
+      run: echo "TZ=America/Chicago" >> "$GITHUB_ENV"
+
+    # TODO: review requirements
+    - name: Sphinx build
+      id: deployment
+      uses: sphinx-notes/pages@v3
+      with:
+        documentation_path: ./docs/source
+        publish: false
+        python_version: "3.11"
+        requirements_path: ./docs/requirements.txt
+
+    - name: Diagnostic
+      run: ls -lAFgh ${{ steps.deployment.outputs.artifact }}
+
+    - name: Upload Docs ZIP file as artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: apsbss-docs
+        path: ${{ steps.deployment.outputs.artifact }}
+
+    - uses: peaceiris/actions-gh-pages@v3
+      if: ${{ github.event.inputs.deploy }}
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ${{ steps.deployment.outputs.artifact }}

.github/workflows/pypi.yml

@@ -0,0 +1,54 @@
+name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+
+on:
+  # Triggers the workflow on push events but only for the main branch
+  push:
+    branches:
+      - main
+    tags:
+      - "*" # all tags
+
+jobs:
+  pypi:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+
+      - name: Install twine
+        run: >-
+          python -m
+          pip install
+          twine
+
+      - name: Check package metadata
+        run: >-
+          twine check dist/*
+
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          verbose: true

apsbss/__init__.py

@@ -1,3 +1,18 @@
+"""Configuration of apsbss package."""
+
+__project__ = "apsbss"
+
+try:
+    from setuptools_scm import get_version
+
+    __version__ = get_version(root="..", relative_to=__file__)
+    del get_version
+except (LookupError, ModuleNotFoundError):
+    from importlib.metadata import version
+
+    __version__ = version(__project__)
+    del version
+
 # -----------------------------------------------------------------------------
 # :author:    Pete R. Jemian
 # :email:     jemian@anl.gov
@@ -7,64 +22,3 @@
 #
 # The full license is in the file LICENSE.txt, distributed with this software.
 # -----------------------------------------------------------------------------
-
-__project__ = u"apsbss"
-__description__ = (
-    u"Read-only interface to information from APS Proposal"
-    u" and ESAF (experiment safety approval form) databases."
-)
-__copyright__ = u"2017-2022, UChicago Argonne, LLC"
-__authors__ = [
-    u"Pete Jemian",
-]
-__author__ = ", ".join(__authors__)
-__institution__ = u"Advanced Photon Source, Argonne National Laboratory"
-__author_email__ = u"jemian@anl.gov"
-__url__ = u"https://BCDA-APS.github.io/apsbss"
-__license__ = u"(c) " + __copyright__
-__license__ += u" (see LICENSE.txt file for details)"
-__platforms__ = "any"
-__zip_safe__ = False
-__exclude_project_dirs__ = ["docs", ]
-__python_version_required__ = ">=3.7"
-
-__package_name__ = __project__
-__long_description__ = __description__
-
-from ._requirements import (
-    learn_requirements,
-)  # lgtm [py/import-own-module]
-
-__install_requires__ = learn_requirements()
-del learn_requirements
-
-__classifiers__ = [
-    "Development Status :: 5 - Production/Stable",
-    "Environment :: Console",
-    "Intended Audience :: Science/Research",
-    "License :: Freely Distributable",
-    "License :: Public Domain",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.7",
-    # "Programming Language :: Python :: 3.8",
-    # "Programming Language :: Python :: 3.9",
-    "Topic :: Scientific/Engineering",
-    "Topic :: Scientific/Engineering :: Astronomy",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Topic :: Scientific/Engineering :: Chemistry",
-    "Topic :: Scientific/Engineering :: Information Analysis",
-    "Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator",
-    "Topic :: Scientific/Engineering :: Mathematics",
-    "Topic :: Scientific/Engineering :: Physics",
-    "Topic :: Software Development :: Embedded Systems",
-    "Topic :: Software Development :: Libraries :: Python Modules",
-    "Topic :: Scientific/Engineering :: Visualization",
-    "Topic :: Software Development",
-    "Topic :: Utilities",
-]
-
-from ._version import get_versions  # lgtm [py/import-own-module]
-
-__version__ = get_versions()["version"]
-del get_versions